contigs_taxonomic_classification
Description¶
Getting per contig taxonomic annotations for metagenomic assembly based on taxonomic classification of predicted proteins with DIAMOND and CAT.
Installation¶
ebi-metagenomics/contigs_taxonomic_classification
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install contigs_taxonomic_classification
Keywords: taxonomic classification, catpack, protein classification, metagenomics
Components¶
This subworkflow uses the following components:
diamond/blastp(module)krona/ktimporttext(module)mgnifypipelinestoolkit/kronatxtfromcatclassification(module)catpack/contigs(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
contigs |
file | The input channel containing file with metagenomic assembly Structure: [ val(meta), path(fasta) ] | *.{fasta, fasta.gz, fa, fa.gz, fna, fna.gz} |
proteins |
file | The input channel containing proteins predicted for the given metagenome CAT assumes that predicted proteins have ids in format |
*.{fasta, fasta.gz, fa, fa.gz, faa, faa.gz} |
cat_db |
path | Directory containing the CAT database produced with catpack/prepare The folder must contain DIAMOND db .dmnd, .fastaid2LCAtaxid, *.taxids_with_multiple_offspring Structure: [ val(meta), path(db_folder) ] | - |
cat_taxonomy_db |
path | Directory containing the tax/ folder of the CAT database produced with catpack/prepare The folder must contain names.dmp and nodes.dmp Structure: [ val(meta), path(tax_db_folder) ] | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
diamond_output |
file | Channel containing a TSV file with matches of predicted proteins to a database Structure: [ val(meta), path(file) ] | *.{txt, txt.gz} |
cat_output |
file | Channel containing a TSV file with taxonomic classification of contigs Structure: [ val(meta), path(file) ] | *.contig2classification.txt |
krona_html |
file | Channel containing a HTML file with Krona plot of taxonomic classification of contigs Structure: [ val(meta), path(file) ] | *.html |
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |